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Altered Gene Expression Along the Glycolysis– Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer Joanna M

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Altered Gene Expression Along the Glycolysis– Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer Joanna M Published OnlineFirst September 3, 2019; DOI: 10.1158/1078-0432.CCR-19-1543 Precision Medicine and Imaging Clinical Cancer Research Altered Gene Expression along the Glycolysis– Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer Joanna M. Karasinska1, James T. Topham1, Steve E. Kalloger1,2, Gun Ho Jang3, Robert E. Denroche3, Luka Culibrk4, Laura M.Williamson4, Hui-Li Wong5, Michael K.C. Lee5, Grainne M. O'Kane6, Richard A. Moore4, Andrew J. Mungall4, Malcolm J. Moore5, Cassia Warren1, Andrew Metcalfe1, Faiyaz Notta3, Jennifer J. Knox6, Steven Gallinger3,6, Janessa Laskin4,5, Marco A. Marra4,7, Steven J.M. Jones4,7, Daniel J. Renouf1,5,8, and David F. Schaeffer1,2,9 Abstract Purpose: Identification of clinically actionable molecular groups were identified: quiescent, glycolytic, cholestero- subtypes of pancreatic ductal adenocarcinoma (PDAC) is key genic, and mixed. Glycolytic tumors were associated with to improving patient outcome. Intertumoral metabolic hetero- the shortest median survival in resectable (log-rank test geneity contributes to cancer survival and the balance between P ¼ 0.018) and metastatic settings (log-rank test P ¼ distinct metabolic pathways may influence PDAC outcome. We 0.027). Patients with cholesterogenic tumors had the lon- hypothesized that PDAC can be stratified into prognostic gest median survival. KRAS and MYC-amplified tumors metabolic subgroups based on alterations in the expression of had higher expression of glycolytic genes than tumors with genes involved in glycolysis and cholesterol synthesis. normal or lost copies of the oncogenes (Wilcoxon rank Experimental Design: We performed bioinformatics analy- sum test P ¼ 0.015). Glycolytic tumors had the lowest sis of genomic, transcriptomic, and clinical data in an integrated expression of mitochondrial pyruvate carriers MPC1 and cohort of 325 resectable and nonresectable PDAC. The resect- MPC2. Glycolytic and cholesterogenic gene expression able datasets included retrospective The Cancer Genome Atlas correlated with the expression of prognostic PDAC subtype (TCGA) and the International Cancer Genome Consortium classifier genes. (ICGC) cohorts. The nonresectable PDAC cohort studies Conclusions: Metabolic classification specific to glycolytic included prospective COMPASS, PanGen, and BC Cancer Per- and cholesterogenic pathways provides novel biological sonalized OncoGenomics program (POG). insight into previously established PDAC subtypes and may Results: On the basis of the median normalized expres- help develop personalized therapies targeting unique tumor sion of glycolytic and cholesterogenic genes, four sub- metabolic profiles. kers capable of predicting treatment response (1). Emerging molec- Introduction ular subtypes of PDAC have defined intertumoral heterogeneity The 5-year survival rate in pancreatic ductal adenocarcinoma at the genome and transcriptome levels (2–6), driving efforts to (PDAC) is less than 10% and remains one of the lowest in all identify clinically relevant biomarker signatures and actionable cancers. Effective therapy is limited by the treatment-refractory genomic alterations (7, 8). However, a better understanding of nature of PDAC and a short supply of clinically validated biomar- how specific cellular tumor progression pathways contribute to 1Pancreas Centre BC, Vancouver, British Columbia, Canada. 2Department of Clinical trial information: Personalized OncoGenomics (POG) Program of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia: Utilization of Genomic Analysis to Better Understand Tumour British Columbia, Canada. 3Ontario Institute for Cancer Research, Toronto, Heterogeneity and Evolution (NCT02155621); Prospectively Defining Metastatic Ontario, Canada. 4Canada's Michael Smith Genome Sciences Centre, Vancouver, Pancreatic Ductal Adenocarcinoma Subtypes by Comprehensive Genomic British Columbia, Canada. 5Division of Medical Oncology, BC Cancer, Vancouver, Analysis (PanGen; NCT02869802); Comprehensive Molecular Characterization British Columbia, Canada. 6University Health Network, University of Toronto, of Advanced Pancreatic Ductal Adenocarcinoma for Better Treatment Selection Toronto, Ontario, Canada. 7Department of Medical Genetics, University of British (COMPASS; NCT02750657). Columbia, Vancouver, British Columbia, Canada. 8Department of Medicine, Corresponding Author: David F. Schaeffer, University of British Columbia, University of British Columbia, Vancouver, British Columbia, Canada. 9Division Vancouver General Hospital, 910 West 10th Avenue, Vancouver V5Z 1M9, of Anatomic Pathology, Vancouver General Hospital, Vancouver, British Colum- Canada. Phone: 604-875-4480; Fax: 604-875-5707; E-mail: bia, Canada. [email protected] Note: Supplementary data for this article are available at Clinical Cancer Clin Cancer Res 2019;XX:XX–XX Research Online (http://clincancerres.aacrjournals.org/). doi: 10.1158/1078-0432.CCR-19-1543 J.M. Karasinska, J.T. Topham, S.E. Kalloger, D.J. Renouf, and D.F. Schaeffer contributed equally to this article. Ó2019 American Association for Cancer Research. www.aacrjournals.org OF1 Downloaded from clincancerres.aacrjournals.org on September 28, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst September 3, 2019; DOI: 10.1158/1078-0432.CCR-19-1543 Karasinska et al. Here, we stratify PDAC into subgroups based on the expression Translational Relevance patterns of glycolytic and cholesterogenic genes, and report their Pancreatic ductal adenocarcinoma (PDAC) has one of the association with survival, mutational, and prognostic gene lowest survival rates of all cancers due in part to a limited expression signatures. knowledge of clinically relevant tumor subtypes that would facilitate better treatment stratification and the development Materials and Methods of new therapies targeting unique molecular signatures. fi Tumor metabolic heterogeneity contributes to clinical out- Patients were enrolled in the ongoing Prospectively De ning come in cancer and represents a potential avenue for the Metastatic Pancreatic Ductal Adenocarcinoma Subtypes by development of personalized treatment strategies. How altera- Comprehensive Genomic Analysis (PanGen, NCT02869802), tions in distinct metabolic pathways influence PDAC outcome the BC Cancer Personalized OncoGenomics program (POG, is not well known. We profiled the expression of glycolytic and NCT02155621), and Comprehensive Molecular Characterization cholesterogenic genes in 325 resectable and non-resectable of Advanced PDAC For Better Treatment Selection (COMPASS, PDAC patients and identified distinct subgroups associated NCT02750657) studies at the BC Cancer Agency (PanGen, POG) with differences in survival and known prognostic pancreatic and Ontario Institute for Cancer Research (COMPASS) as tumor subtypes. Our findings demonstrate that distinct met- described previously (7, 29). The PanGen and POG studies were abolic gene expression pathways may provide a functional approved by the University of British Columbia Research Ethics correlate to transcriptome-based pancreatic cancer subtypes, Committee (REB# H12-00137, H14-00681, H16-00291) and the which may enable the development of subtype-specific treat- COMPASS study was approved by the University Health Network ment strategies targeting unique metabolic vulnerabilities. Research Ethics Board (REB# 15-9596). The studies were conducted in accordance with international ethical guidelines. Written informed consent was obtained from each patient prior to genomic profiling. PDAC prognostic stratification is needed to enable customized Whole genome and transcriptome sequencing treatment design and novel therapeutics development. POG and PanGen samples were subjected to whole genome Oncogene-driven metabolic adaptations allow cancer cells to and transcriptome sequencing as described previously (30). survive and thrive in the tumor microenvironment (9). A pan- Briefly, fresh tumor biopsies were sequenced to a depth of cancer analysis of global metabolic pathways showed that tumor approximately 80Â, with approximately 200 million reads metabolic heterogeneity is associated with survival, somatic driver generated for transcriptomes. RNA sequencing (RNA-seq) mutations, and tumor subtypes (10), but whether heterogeneity libraries were prepared using inactive magnetic bead-based in distinct metabolic pathways can be used to stratify PDAC into mRNA purification. RNA-seq was performed on COMPASS clinically relevant subgroups has not been well established. A vast samples as described previously (7). majority of PDACs harbor oncogenic KRAS and loss-of-function TP53 mutations (6), in addition to prevalent hypoxia (11), which TCGA (PAAD-US) and ICGC (PACA-CA) data – are known inducers of the glycolytic pathway in cancer (12 15), Normalized RNA-seq data (sequence-based gene expression; and glycolysis contributes to tumor progression and chemoresis- GRCh37) for all available PAAD-US (n ¼ 142) and PACA-CA tance in PDAC (13, 16, 17). The effects of glycolysis on tumor (n ¼ 234) samples were downloaded from the ICGC data portal progression can be diminished by diverting the metabolite pyru- (dcc.icgc.org/) on November 8, 2018 (ICGC data release 27). vate from conversion to lactate in part through transport into the PACA-CA samples were filtered to exclude any samples labeled mitochondria via the activity of the mitochondrial pyruvate as cell lines, xenografts, metastatic, normal, or non-laser micro- complex (MPC), comprised of pyruvate carrier
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